I think in freeview the syntax would be:
freeview -f lh.inflated:label=lh.your_ROI.label
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel
wrote:
Hi Bruce,
Sorry for so many responses. I figured it out that I can visualize it using
tksurfer.
Besides this, can I visualize it in freeview, CARET, or some other tools? My
goal is to display the ROI on a fsaverage inflated surface.
If it can be done in freeview, could you give me some instruction? In
freeview, I found that I can only load ROI after I load a volume, but not
after I load a surface.
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/16/13 10:14 AM, "Yang, Daniel" <yung-jui.y...@yale.edu> wrote:
Hi Bruce,
Thanks so much! So I ran the following and obtained all the DK ROI
labels.
mri_annotation2label --subject fsaverage --hemi rh --outdir
<my_output_dir>
Then, I am wondering how I can use the label files. For example, can I
overlay it on a brain in fslview?
The label file has many lines. Could you suggest what document I can
read in order to interpret it? One of them is like, "1530 47.244
-41.285 -1.841 0.0000000000".
Thanks for your help!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/16/13 9:32 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Hi Daniel
you could use the DK annotation of the fsaverage brain, which I
think we
supply. The atlas itself is a compilation of multiple statistics
and not
easily visualizable (except for the prior probability I guess).
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel wrote:
Hi Bruce,
I am sorry, I mean, is there a DK atlas on a standard
template brain (like
MNI 152)? sorry, I don't know how DK atlas works. Is it a
probabilistic
atlas, or dependent on the exact folding pattern of the
unique individual?
(I guess it's the latter).
I'd like to generate a ROI brain mask for a specific
region on the DK atlas,
independent of the individual I ran. Having said so, I
guess I can just run
recon-all on a MNI 152 brain, so that I can get the ROI
maps.
Thanks,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/15/13 8:43 PM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Daniel
sorry, can you clarify? The DK atlas is estimated on every
brain that
you
run recon-all on and stored in the label directory. Is
that what you
want?
cheers
Bruce
On Mon, 15 Jul 2013,
Yang, Daniel wrote:
Dear FreeSurfer Expert,
I would like to draw the specific ROI of the DK atlas (not
specific
individual, but this ROI in general). I'm wondering how
this ROI
can be
extracted/created as a mask so that I can draw it on the
brain
using some
software?
Could you please advise?
Thanks a lot,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
The information in this e-mail is intended only for the
person to whom
it is
addressed. If you believe this e-mail was sent to you in
error and the
e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was
sent to you
in error
but does not contain patient information, please contact
the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
